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- PDB-6rci: Crystal structure of REXO2 -

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Basic information

Entry
Database: PDB / ID: 6rci
TitleCrystal structure of REXO2
ComponentsOligoribonuclease, mitochondrial
KeywordsHYDROLASE / Mitochondria / Oligoribonuclease / REXO2
Function / homology
Function and homology information


Mitochondrial RNA degradation / Hydrolases; Acting on ester bonds; Exonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / 3'-5'-DNA exonuclease activity / nucleotide metabolic process / nucleobase-containing compound metabolic process / 3'-5' exonuclease activity / mitochondrial intermembrane space / 3'-5'-RNA exonuclease activity / nucleic acid binding / mitochondrial matrix ...Mitochondrial RNA degradation / Hydrolases; Acting on ester bonds; Exonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / 3'-5'-DNA exonuclease activity / nucleotide metabolic process / nucleobase-containing compound metabolic process / 3'-5' exonuclease activity / mitochondrial intermembrane space / 3'-5'-RNA exonuclease activity / nucleic acid binding / mitochondrial matrix / focal adhesion / nucleolus / magnesium ion binding / mitochondrion / nucleus / cytoplasm
Similarity search - Function
Oligoribonuclease / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
Oligoribonuclease, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSpahr, H. / Nicholls, T.J. / Larsson, N.G. / Gustafsson, C.M.
Funding support Germany, Sweden, 4items
OrganizationGrant numberCountry
Max Planck Society Germany
Swedish Research Council Sweden
Knut and Alice Wallenberg Foundation Sweden
European Research Council
CitationJournal: Mol.Cell / Year: 2019
Title: Dinucleotide Degradation by REXO2 Maintains Promoter Specificity in Mammalian Mitochondria.
Authors: Nicholls, T.J. / Spahr, H. / Jiang, S. / Siira, S.J. / Koolmeister, C. / Sharma, S. / Kauppila, J.H.K. / Jiang, M. / Kaever, V. / Rackham, O. / Chabes, A. / Falkenberg, M. / Filipovska, A. / ...Authors: Nicholls, T.J. / Spahr, H. / Jiang, S. / Siira, S.J. / Koolmeister, C. / Sharma, S. / Kauppila, J.H.K. / Jiang, M. / Kaever, V. / Rackham, O. / Chabes, A. / Falkenberg, M. / Filipovska, A. / Larsson, N.G. / Gustafsson, C.M.
History
DepositionApr 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 18, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oligoribonuclease, mitochondrial
B: Oligoribonuclease, mitochondrial


Theoretical massNumber of molelcules
Total (without water)41,7902
Polymers41,7902
Non-polymers00
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-5 kcal/mol
Surface area15480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.164, 128.492, 170.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Oligoribonuclease, mitochondrial / RNA exonuclease 2 homolog / Small fragment nuclease


Mass: 20894.963 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REXO2, SFN, SMFN, CGI-114 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2
References: UniProt: Q9Y3B8, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 100 mM Hepes pH 7.0, 200 mM sodium malonate, and 20 % polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2→22.74 Å / Num. obs: 51266 / % possible obs: 98.8 % / Redundancy: 3.428 % / Biso Wilson estimate: 39.42 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.108 / Χ2: 1.345 / Net I/σ(I): 8.47
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.123.3520.7861.2681880.5640.93597.8
2.12-2.273.5120.4912.1879040.80.5899.8
2.27-2.453.3640.3433.0972030.8730.40898.8
2.45-2.683.5360.2175.0167270.9480.25599.3
2.68-2.993.5370.1358.1460820.9790.15999.4
2.99-3.453.3460.08113.4852930.9920.09798.8
3.45-4.223.4330.05520.6545170.9950.06599
4.22-5.943.290.04424.5434460.9970.05297.2
5.94-22.743.3970.03727.2319060.9980.04496.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→22.74 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.185 / SU Rfree Blow DPI: 0.157 / SU Rfree Cruickshank DPI: 0.152
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1118 4.1 %RANDOM
Rwork0.199 ---
obs0.2 27274 99.1 %-
Displacement parametersBiso max: 116.62 Å2 / Biso mean: 48.63 Å2 / Biso min: 17.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.8681 Å20 Å20 Å2
2--6.3841 Å20 Å2
3----7.2522 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: final / Resolution: 2→22.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2663 0 0 247 2910
Biso mean---51.49 -
Num. residues----326
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1189SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes834HARMONIC5
X-RAY DIFFRACTIONt_it5349HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion353SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5852SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5349HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9687HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion3.58
X-RAY DIFFRACTIONt_other_torsion15.6
LS refinement shellResolution: 2→2.01 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3291 23 4.21 %
Rwork0.2316 523 -
all0.2364 546 -
obs--87.62 %

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